Phylogenetic lineage studies have demonstrated that serotype III GBS associated with human disease derive largely from two distinct lineages. We compared the phylogenetic lineages of invasive type III group B streptococci to those of colonizing strains in order to determine lineages associated with invasive disease. Isolates from 29 infants with early-onset disease and from 196 colonized infants, collected in a prospective, multicenter study, were assigned a sequence type (ST) by multi-locus sequence typing. Overall, 54.5% of the isolates were in the ST-19 complex and 40.4% were in the ST-17 complex. Invasive strains were more likely to be in the ST-17 complex compared to colonizing strains (59% vs. 38%, P=0.03). After adjusting for potential confounders, the ST-17-complex was more likely to be associated with early-onset disease than were other lineages [odds ratio = 2.51, 95% confidence interval 1.02 - 6.20]. These data support the hypothesis that ST-17 complex GBS are more virulent than other serotype III GBS.